Friday, December 23, 2011

modeling neuron; how to make a simulated model neuron; software, tools free package, open source; Computational Neuroscience : simulation, neuroengineering, neurophysics; modeliser le "neurone"; NEURON, GENESIS, NEUROCAL (Matlab)

Using well-characterized preparations allows simulation of the cable equation and several freely available packages are designed to assist with cable modeling.
Trois logiciels pour la modélisation électrique du "neurone":
(old, before 2008:
-Neurocal is a simplified package written in MATLAB that is very easy to use and modify.
 Combining easily modeled, well-documented neurological preparations with simple lab experiments and accurate, easy to use active cable equation simulators is a powerful application of the engineering methodology of simulate, design, fabricate, and test.

1-NEURONThe alpha version directory also contains source code for the alpha versions, which you can download and compile on your own machine. After downloading the nrn-nn.alpha.tar.gz and iv-mm.tar.gz from the alpha version directory, follow the same instructions as for compiling the standard distribution for your operating system
    OS X
    MSWin (95 and up)

 GENESIS (short for GEneral NEural SImulation System) is a general purpose simulation platform that was developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and systems-level models. As such, GENESIS, and its version for parallel and networked computers (PGENESIS) was the first broad scale modeling system in computational biology to encourage modelers to develop and share model features and components.
If you would like become a GENESIS developer, please send a request to with the subject "New Developer Request."
The following operating systems are currently supported for developer installations of GENESIS: 

Simulation describing the electrophysiological behavior of a biological neuron (nerve cell). Two sets of membrane kinetics are included: Hodgkin-Huxley and Schwarz for unmyelinated and myelinated axons. Straight forward approach makes for easy use, somewhat easier than Neuron and Genesis.Very well layout in plot GUI allows multiple variables to be graphed, a real plus over Neuron. If inproved on would like to see parabolic bursting added non the less an outstanding project for a freebee.

MATLAB ---> multiplatform
Carnevale, N.T. and M.L. Hines, The Neuron book. 2006, Cambridge, UK; New York:
Cambridge University Press. xix, 457p.

Bower, J.M. and D. Beeman, The book of Genesis: exploring realistic neural models with the
GEneral NEural SImulation System. 1998. Springer-Verlag New York, Inc. New York.

Zeng, L. and M.D. Dominique, Extracellular voltage profile for reversing the recruitment
order of peripheral nerve stimulation: a simulation study. Journal of Neural Engineering,
2004, 4: 202.

Other  Stand Alone Programs for use in Computational Neuroscience:
The Gencompress Utility
Mesh Generator for Neurons
RALLPACKS version 1.1
Ref (review):
Basham E, Yang Z, Tchemodanov N, Liu W. Magnetic stimulation of neural tissue: techniques and system design. Implantable Neural Prostheses 1 2009;293–351.
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